feat(eyevolume): enable use of EyeVolume in eyelab

.pre-commit-config.yaml

@@ -5,6 +5,12 @@ repos:
   - id: trailing-whitespace
   repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.1.0
+- hooks:
+  - id: isort
+    args: ["--profile", "black"]
+    name: isort (python)
+  repo: https://github.com/pycqa/isort
+  rev: 5.10.1
 - hooks:
   - id: black
   repo: https://github.com/psf/black

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 <!--next-version-placeholder-->
 
+## v0.5.0 (2022-03-02)
+### Feature
+* **eyevolume.py:** Enable custom intensity transformation for OCT data ([`761dd5a`](https://github.com/MedVisBonn/eyepy/commit/761dd5a4a360ca46d79ff2074b2644b4c2fd8ca4))
+
 ## v0.4.1 (2022-02-17)
 ### Fix
 * **EyeVolume:** Fix B-scan iteration; enable setting layer heights from EyeBscan ([`f982d68`](https://github.com/MedVisBonn/eyepy/commit/f982d687a7834922866377b70a755e253c785880))

CITATION.cff

@@ -0,0 +1,49 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: eyepy
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Olivier
+    family-names: Morelle
+    email: oli4morelle@gmail.com
+    orcid: 'https://orcid.org/0000-0001-6404-2726'
+    affiliation: >-
+      University of Bonn - Bonn-Aachen International
+      Center for Information Technology (b-it) /
+      University Hospital Bonn - Department of
+      Ophthalmology
+identifiers:
+  - type: url
+    value: 'https://github.com/MedVisBonn/eyepy/tree/v0.5.0'
+repository-code: 'https://github.com/MedVisBonn/eyepy/tree/v0.5.0'
+abstract: >-
+  Eye imaging data from different device vendors
+  often come in different file formats. Additionally,
+  public datasets often have their own way of storing
+  data for distribution. The lack of documentation
+  for many device-specific formats is a problem
+  already when working with a single data source
+  while the pure amount of different formats slows
+  down everyone trying to use data from multiple
+  sources.
+
+  This Python package aims at providing a unified
+  interface to a wide variety of eye imaging formats
+  and the execution of standard tasks such as data
+  visualization and quantification on ETDRS grids.
+  Thereby, it enables the development of
+  device-independent software and algorithms.
+keywords:
+  - OCT
+  - Drusen
+  - Heidelberg
+  - HEYEX
+  - ETDRS
+license: MIT
+version: v0.5.0
+date-released: '2022-03-02'

README.md

@@ -18,6 +18,7 @@ pin the version in your project requirements.
 * Quantify voxel annotations on a customizable circular grid
 * Plot annotated localizer
 * Plot annotated B-scans
+* Save and load EyeVolume objects
 
 ## Getting Started
 
@@ -81,9 +82,9 @@ import eyepy as ep
 # Import example data
 ev = ep.data.load("drusen_patient")
 drusen_map = ep.drusen(ev.layers["RPE"], ev.layers["BM"], ev.shape, minimum_height=2)
-ev.set_volume_map("drusen", drusen_map)
+ev.add_voxel_annotation(drusen_map, name="drusen")
 
-fig, axes = plt.subplots(1,2, figsize=(5,10))
+fig, axes = plt.subplots(1, 2, figsize=(5, 10))
 
 # Configure quantification grid for drusen quantification
 ev.volume_maps["drusen"].radii = [1.5, 2.5]
@@ -117,3 +118,4 @@ ax.axis("off")
 # Related Projects:
 
 + [OCT-Converter](https://github.com/marksgraham/OCT-Converter): Extract raw optical coherence tomography (OCT) and fundus data from proprietary file formats. (.fds/.fda/.e2e/.img/.oct/.dcm)
++ [eyelab](https://github.com/MedVisBonn/eyelab): A GUI for annotation of OCT data based on eyepy

eyepy/__init__.py

@@ -3,28 +3,25 @@
 
 __author__ = """Olivier Morelle"""
 __email__ = "oli4morelle@gmail.com"
-__version__ = "0.4.1"
+__version__ = "0.5.0"
 
 from eyepy.core import (
-    EyeEnface,
-    EyeVolume,
     EyeBscan,
-    EyeData,
-    EyeVolumeMeta,
+    EyeBscanLayerAnnotation,
     EyeBscanMeta,
+    EyeEnface,
+    EyeEnfaceAreaAnnotation,
     EyeEnfaceMeta,
-    EyeVolumeVoxelAnnotation,
+    EyeVolume,
     EyeVolumeLayerAnnotation,
+    EyeVolumeMeta,
+    EyeVolumeVoxelAnnotation,
 )
-
 from eyepy.io import (
-    import_heyex_xml,
-    import_heyex_vol,
     import_bscan_folder,
     import_duke_mat,
+    import_heyex_vol,
+    import_heyex_xml,
     import_retouch,
 )
-
 from eyepy.quantification import drusen
-
-import eyepy.data as data

eyepy/config.py

@@ -12,7 +12,22 @@
 line_kwargs = {"linewidth": 0.2, "linestyle": "-", "color": "green"}
 
 # Colors for different Layers
-# x = sns.color_palette("husl", 17)
-# color_palette = sns.color_palette(x[::3] + x[1::3] + x[2::3])
-# layer_colors = {key: color_palette[value] for key, value in SEG_MAPPING.items()}
-layer_colors = defaultdict(lambda: "red")
+_layer_colors = {
+    "BM": "F77189",
+    "RPE": "97A431",
+    "PR1": "36ADA4",
+    "EZ": "36ADA4",
+    "PR2": "A48CF4",
+    "IZ": "A48CF4",
+    "ELM": "E68332",
+    "ONL": "50B131",
+    "OPL": "38AABF",
+    "INL": "E866F4",
+    "IPL": "BB9832",
+    "GCL": "34AF84",
+    "RNFL": "3BA3EC",
+    "NFL": "3BA3EC",
+    "ILM": "F668C2",
+}
+
+layer_colors = defaultdict(lambda: "FF0000", **_layer_colors)

eyepy/core/__init__.py

@@ -1,6 +1,5 @@
 # from annotations import Annotation, LayerAnnotation
-from .eyemeta import EyeVolumeMeta, EyeBscanMeta, EyeEnfaceMeta
-from .eyebscan import EyeBscan
-from .eyedata import EyeData
-from .eyevolume import EyeVolume, EyeVolumeVoxelAnnotation, EyeVolumeLayerAnnotation
-from .eyeenface import EyeEnface
+from .eyebscan import EyeBscan, EyeBscanLayerAnnotation
+from .eyeenface import EyeEnface, EyeEnfaceAreaAnnotation
+from .eyemeta import EyeBscanMeta, EyeEnfaceMeta, EyeVolumeMeta
+from .eyevolume import EyeVolume, EyeVolumeLayerAnnotation, EyeVolumeVoxelAnnotation

eyepy/core/eyebscan.py

@@ -1,51 +1,66 @@
-import collections
+from typing import List
 
+import matplotlib.pyplot as plt
 import numpy as np
+
 from eyepy import config
-import matplotlib.pyplot as plt
+from eyepy.core.utils import DynamicDefaultDict
 
 
-class EyeBscanLayers:
-    def __init__(self, eyebscan):
-        self.index = eyebscan.index
-        self.volume = eyebscan._volume
+class EyeBscanLayerAnnotation:
+    def __init__(self, eyevolumelayerannotation, index):
+        self.eyevolumelayerannotation = eyevolumelayerannotation
+        self.volume = eyevolumelayerannotation.volume
+        self.index = index
 
-    def __getitem__(self, item):
-        return self.volume.layers[item].data[-(self.index + 1)]
+    @property
+    def name(self):
+        return self.eyevolumelayerannotation.meta["name"]
 
-    def __setitem__(self, key, value):
-        self.volume.layers[key].data[-(self.index + 1), :] = value
+    @name.setter
+    def name(self, value: str):
+        self.eyevolumelayerannotation.meta["name"] = value
+
+    @property
+    def data(self):
+        return self.eyevolumelayerannotation.data[-(self.index + 1), :]
+
+    @data.setter
+    def data(self, value):
+        self.eyevolumelayerannotation.data[-(self.index + 1), :] = value
+
+    @property
+    def knots(self):
+        return self.eyevolumelayerannotation.knots[self.index]
+
+    @knots.setter
+    def knots(self, value: List):
+        self.eyevolumelayerannotation.knots[self.index] = value
 
 
 class EyeBscan:
     def __init__(self, volume: "EyeVolume", index: int):
         self.index = index
-        self._volume = volume
+        self.volume = volume
 
-        self._bscan_layers = EyeBscanLayers(self)
+        self.layers = DynamicDefaultDict(
+            lambda x: EyeBscanLayerAnnotation(self.volume.layers[x], self.index)
+        )
+        self.area_maps = DynamicDefaultDict(
+            lambda x: self.volume.volume_maps[x].data[self.index]
+        )
 
     @property
     def meta(self):
-        return self._volume.meta["bscan_meta"][self.index]
+        return self.volume.meta["bscan_meta"][self.index]
 
     @property
     def data(self):
-        return self._volume.data[self.index]
-
-    @property
-    def layers(self):
-        return self._bscan_layers
+        return self.volume.data[self.index]
 
     @property
     def ascan_maps(self):
-        return self._volume.ascan_maps[self.index]
-
-    @property
-    def area_maps(self):
-        return {
-            name: self._volume.volume_maps[name].data[self.index]
-            for name in self._volume.volume_maps.keys()
-        }
+        return self.volume.ascan_maps[self.index]
 
     @property
     def shape(self):
@@ -89,12 +104,12 @@ def plot(
         if layers is None:
             layers = []
         elif layers is True:
-            layers = self.layers.keys()
+            layers = self.volume.layers.keys()
 
         if areas is None:
             areas = []
         elif areas is True:
-            areas = self.area_maps.keys()
+            areas = self.volume.volume_maps.keys()
 
         if ascans is None:
             ascans = []
@@ -138,11 +153,10 @@ def plot(
                 cmap="Reds",
                 interpolation="none",
             )
-
         for layer in layers:
             color = config.layer_colors[layer]
 
-            layer_data = self.layers[layer]
+            layer_data = self.layers[layer].data
             # Adjust layer height to plotted region
             layer_data = layer_data - region[0].start
             # Remove layer if outside of region
@@ -153,7 +167,7 @@ def plot(
 
             ax.plot(
                 layer_data,
-                color=color,
+                color="#" + color,
                 label=layer,
                 **layer_kwargs,
             )